Phylogenetics within <i>Camassia</i> (Asparagaceae): examining difficult taxonomy and unusual variation using genomic restriction-site-associated DNA sequencing data

Increasing the number of sampled loci improved phylogenetic signal despite concurrent increases in missing data. Each taxon was generally cohesive on the phylogenies, but some species and subspecies were not monophyletic. Results suggest that there was an early separation of <i>C. howellii</i> and <i>C. leichtlinii</i> from the rest of the genus during diversification. Different analysis parameters supported either a clade of both species as sister to the remainder of the genus, or <i>C. howellii</i> alone as sister. Relationships among all relatively deep clades within the genus were well supported. Within species, <i>C. leichtlinii</i> had particularly robust support for relationships compared to others in <i>Camassia</i>, and geographic patterns corresponding to the diversification of some subclades were resolved. The eight subspecies of <i>C. quamash</i> largely formed two main clades. Although most subspecies showed sufficient phylogenetic, morphological, or ecological distinctiveness to maintain recognition, we recommend synonymizing <i>C. quamash</i> ssp. <i>intermedia</i> into <i>C. quamash</i> ssp. <i>maxima</i>. Some outlier individuals of <i>C. quamash</i> were resolved with other species. For example, the status of <i>C. quamash</i> ssp. <i>utahensis</i> was called into question by a well-supported division placing two populations with <i>C. cusickii</i>. In the disjunct species complex distributed further east in North America (<i>C. scilloides</i>+), results confirmed at least one progenitor-derivative species pair (<i>C. angusta</i> arising from <i>C. scilloides</i>) and some evidence for a potential new taxon closely related to <i>C. angusta</i>. Overall, these taxa have diversified in traits that can result in genetic isolation, such as differences in flowering seasons and ecological preferences, but there also are indications of some continued gene flow among both subspecies and species.